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Variant: NM_005629.4(SLC6A8):c.1141G>C (p.Gly381Arg)

CA256011

11697 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: c1a4361d-9e35-418a-a3f0-64f450c5c95a

HGVS expressions

NM_005629.4:c.1141G>C
NM_005629.4(SLC6A8):c.1141G>C (p.Gly381Arg)
NC_000023.11:g.153693586G>C
CM000685.2:g.153693586G>C
NC_000023.10:g.152959041G>C
CM000685.1:g.152959041G>C
NC_000023.9:g.152612235G>C
NG_012016.1:g.10290G>C
NG_012016.2:g.10290G>C
ENST00000253122.10:c.1141G>C
ENST00000253122.9:c.1141G>C
ENST00000413787.1:c.257G>C
ENST00000430077.6:c.796G>C
ENST00000442457.1:c.195G>C
ENST00000457723.1:c.125G>C
ENST00000467402.1:n.240G>C
ENST00000485324.1:n.1174G>C
NM_001142805.1:c.1111G>C
NM_001142806.1:c.796G>C
NM_005629.3:c.1141G>C
NM_001142805.2:c.1111G>C

Pathogenic

Met criteria codes 5
PM2_Supporting PS3_Supporting PP3 PP4_Strong PP1_Strong

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC6A8 Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_005629.4:c.1141G>C variant in SLC6A8 is a missense variant that is predicted to lead to the substitution of a glycine for an arginine at amino acid 381 (p.Gly381Arg). This variant has been previously reported in one family with 5 affected males with elevated urinary creatine/creatinine and deficient creatine uptake in cultured fibroblasts (PP4_Strong) and segregated with disease in this family (PP1_Strong) (PMID: 11898126). This variant was reported to result in reduced (<10% of wild-type) creatine transport activity in SLC6A8 deficient fibroblasts (PMID: 22281021) (PS3_Supporting). In addition, the variant was shown to result in altered splicing via RT-PCR analysis (PMID: 11898126). The variant is absent in gnomAD v2.1.1. (PM2_Supporting). The computational predictor REVEL gives a score of 0.923 which is above the threshold of 0.75, evidence that correlates with impact to SLC6A8 function (PP3). There is a ClinVar entry for this variant (Variation ID 11697, zero-star review status), with one submitter classifying the variant as pathogenic. In summary, this variant meets criteria to be classified as pathogenic for creatine transporter deficiency. SLC6A8-specific criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): PS3_Supporting, PM2_Supporting, PP3, PP1_Strong, PP4_Strong. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on March 28, 2024).
Met criteria codes
PM2_Supporting
The variant is absent in gnomAD v2.1.1. (PM2_Supporting).
PS3_Supporting
This variant was reported to result in reduced (<10% of wild-type) creatine transport activity in SLC6A8 deficient fibroblasts (PMID: 22281021) (PS3_Supporting).
PP3
The computational predictor REVEL gives a score of 0.923 which is above the threshold of 0.75, evidence that correlates with impact to SLC6A8 function (PP3).
PP4_Strong
This variant has been previously reported in one family with 5 affected males with elevated urinary creatine/creatinine and deficient creatine uptake in cultured fibroblasts (PP4_Strong) and segregated with disease in this family (PP1_Strong) (PMID: 11898126).
PP1_Strong
This variant has been previously reported in one family with 5 affected males with elevated urinary creatine/creatinine and deficient creatine uptake in cultured fibroblasts (PP4_Strong) and segregated with disease in this family (PP1_Strong) (PMID: 11898126).
Approved on: 2024-03-28
Published on: 2024-03-28
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